Like many other older churchmen, politicians and businessmen in Argentina, Cardinal Jorge Mario Bergoglio has been questioned by some for his role during this country’s bloody 1976–83 military dictatorship, when tens of thousands of young dissidents were made to “disappear” in the death camps set up by the generals who ruled the country.

The Catholic Church in Argentina realized that its behavior during that dark period was so unsaintly that in 2000 it made a public apology for its failure to take a stand against the generals. “We want to confess before God everything we have done badly,” Argentina’s Episcopal Conference said at that time. “We share everyone’s pain and once again ask the forgiveness of everyone we failed or didn’t support as we should have,” Argentina’s bishops said in a statement again last year after former dictator Jorge Videla, now serving a life sentence, claimed in an interview that he had received the blessing of the country’s top clergymen for the actions of his regime.

Since he was anointed cardinal by Pope John Paul II in Rome in 2000, Jorge Bergoglio has had to contend with repeated allegations over his actions — and inaction — in the years of what is called the “Dirty War.” Those claims have resurfaced now that he has become Pope Francis, the first Pontiff from the New World.

Even before his election as Pope, Bergoglio has always been a popular and admired figure among Argentine Catholics. The general criticism against him has been that raised against most prominent personalities of the period of junta rule: that he perhaps did not do enough at the time to try to stop the generals, that he did not speak out publicly about the thousands of desaparecidos — the disappeared who vanished without a trace and whose mothers protested for answers in a plaza in Buenos Aires. Most Argentines are aware, however that if Bergoglio had been an active critic of the regime, he would almost certainly not have lived to become Pope. Other churchmen at the time were quickly murdered by the country’s merciless generals.

Nevertheless, there is one specific charge against Bergoglio and it involves the kidnapping of two priests, Orlando Yorio and Francisco Jalics — both Jesuits, members of the Society of Jesus, a Catholic religious order that the future Pope led in Argentina from 1973–79. The duo were taken by Navy officers in May 1976 and held under inhumane conditions allegedly because of the missionary work they conducted in the country’s slums. The chief proponent of the accusation has been Argentine journalist Horacio Verbitsky, who has authored a series of books on the history of the Argentine Catholic Church. In El Silencio (“The Silence”), Verbitsky says that Bergoglio withdrew his order’s protection from the two priests, giving the military a green light for their abduction.

Bergoglio has called the allegation “slander” and says that, on the contrary, he moved behind the scenes to save the lives of the two priests. He claims to have met with Videla and Admiral Emilio Massera, the two most important members of the military junta that ruled the country, to obtain their release, Bergoglio told his biographer Sergio Rubin in 2005. “I never believed [the two priests] were involved in subversive activies,” Bergoglio said. “But because of their work with some priests in the slums they were exposed to the paranoia of the witch hunt.” Bergoglio said he moved fast to save their lives. “That same night when I heard of the kidnappings I started to move. I saw Videla twice and I saw Massera. In one of my attempts to meet Videla I found out who the military chaplain was who gave mass to Videla and convinced him to call in sick and managed to be named to replace him.” Bergoglio said that after the mass he managed to speak to Videla about the case, which would not have been an easy task at the time, given the climate of fear that reigned over these issues in Argentina then.

The priests were ultimately released five months later. Yorio has since died and Jalics has retired to seclusion in a German monastery. Bergoglio, described as a “humanist” by his many followers in Argentina and a man who has consistently defended the poor, claims he even helped one dissident who looked physically like him flee the country by giving him his own identity papers.

One lawyer, Myriam Bregman, attempted to open a legal case against Bergoglio for the kidnapping of the priests but it ultimately failed for lack of sufficient legal evidence. She says was frustrated by a lack of cooperation by the Cardinal. “Bergoglio refused to come testify in court,” she recalls, making use of Argentine legislation that permits ministers of the church to choose where to make their statements. “He finally accepted to see us in an office alongside Buenos Aires Cathedral sitting underneath a tapestry of the Virgin Mary, it was an intimidating experience, we were very uncomfortable intruding in a religious building.” Meanwhile, Verbitsky says he is saddened that the man he believes did not rise to the challenge of facing the dictatorship squarely in the eye has become Pope. “It is terrible to see how he is rewarded,” says the journalist.

Suspicions and allegations like those of Bregman and Verbitsky are by no means universally held. They are roundly denied, for example, by Argentina’s 1980 Nobel Peace Prize winner Adolfo Perez Esquivel, himself a victim of the dictatorship, tortured and held without trial for 14 months in 1977. “There were bishops who were accomplices, but not Bergoglio,” Perez Esquivel says. “There is no link relating him to the dictatorship. Bergoglio is questioned because it is said he did not do enough to get two priests out of prison while he was the superior of the Jesuits. But I know personally that many bishops requested the military junta to release prisoners and priests but they were not heeded.”

In any event, Bergoglio has lived with the allegations for years and, as Pope Francis, will have to do so for many more to come.